Hello Wayne,
You wrote: [...]
>One thing that does puzzle me is how the chromosomes of
>related species can be so different in there arrangement
>in the respective genomes. For example, morphologically,
>the mouse and the rat look quite similar. Yet the
>arrangement of the genes on the respective organisms seems
>very different. Likewise, often the introns also seem to
>have almost no homology.

I think that in many cases, rearrangements of genes had
relatively little effect on gene function. So variations in
the gene order or location of genes on particular chromosomes
could be more easily accommodated. Likewise introns and
transposons, as long as they had lesser effects overall. Lab
observations and inferences from surveys of organisms lend
some support to these possibilities (Of course there will always
be exceptions -- I don't think predictions can be made in
specific instances). Although the relationships between
genetic variation and various factors such as biochemical,
behavioral and morphological similarities may be tentative and
difficult to determine, it's the time since divergence that
remains the strongest correlating factor.

>I don't say this to argue, but unlike Li's lucid
>description of the globin gene, I find the speciation
>process quite baffling. In my ignorance at least, I
>would have expected it to be rather similar.

Well, there are many different biochemical routes to speciation.
David Campbell described chromosomal rearrangements as one
driver. That process has actually been observed to give
rise to different species in plants (polyploidy). However,
rearrangements (chromosome fusion, splitting, inversion
& etc.) do not necessary produce mating barriers, and so
it is hard to point to a particular change long after the
fact and say, "Aha! That's what caused speciation." For example,
sometime during human evolution two separate chromosome in apes
fused to produce a single chromosome in humans. That may or
may not have introduced a reproductive barrier.

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Moorad wrote (in response to Wayne's question:
>This sort of discussions always bring to mind that what one is
>trying to do is to find a metric in the DNA space. Just like we
>do when we define distance in ordinary space. I do not think
>such a metric has been found.

Exactly. The problem currently exceeds our abilities. Not only
is there insufficient understanding about the workings of
basic biology but also the computational capacity. The best
test remains observation. Currently there are a few groups that
are attempting to model the metabolism of an entire cell _in silico_.
They will definitely find some interesting things, particularly
finding unknown regulatory pathways when their models diverge from
observations. And although it's a necessary and worthwhile effort
even if they only manage to scratch the surface, I'm not optimistic
about the likelihood of overall success within the next few decades.

Still, if one cannot perfectly "retro-predict" each step in
a species evolution, perhaps there are other approaches to
try. For example, we can sometimes focus on specific components
and ask if a particular change can be achieved. Thus one might
be able to examine "possibility" and "plausibility" in relatively
simple systems.